If you mean the bootloader:
You can simply upload the new bootloader ( using an ISP & IDE ).
If you do not use a bootloader ( ISP using AVR tools ) it should erase the flash before upload anyway, but not important.
ISP: In system programmer: https://www.google.com/search?q=in+system+programmer+avr
Or if you are referring to the actual sketch, simply hit the upload button.
Give a bit more information into what exactly you need to do. Do you have a copy of the Arduino IDE & code for the 3d printer? Have you used Arduino before or is this completely new to you ( have no idea where to start )?